RetrogeneDB ID: retro_ptro_2049

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:47740044..47741162(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: BIN2
• Ensembl ID: ENSPTRG00000004954
• Aliases: None
• Description: bridging integrator 2 [Source:HGNC Symbol;Acc:1053]

Sequence

>retro_ptro_2049
AAACTACTAGAGGAGTTGCCTATTCTTTACAATAGTCATACTGGCTCGATGTGACCATCTTCCAAAACATTTCCAACTTG
AGGGATGTCTTCTACAGGGAAATGAGCAAGCTGAACCACAATCTCTCCGAGGTGATGAGCAAACTGGAGAAGCAACATTC
CAGTAAAGTCTTTGTGGTGAAGAGACTATCAAGCAGCAGCAGGCGCTCTTTAGTCATTTCTCCCCCAGTTCGAACATCTA
CAGTCTCCAGTCCACTTACCTCACCTACTAGTCCCTCTACACTTTCCTCAAAGAGTAAGAGTGAATCCGTCTCAGCAACT
GAAGATCTGGCACCTGATGCAGCCCAGGGGGAAGACAATTCTTAGATCAAGGAGCTCTTAGAAGATGAGGAAATAGGGAA
GGAAGGATCTGAAGCAAGCTCCTCTGAGGAAGAAGAGCCTCTACTAACCTGCAATGGCCCCTCCCAGGCCCAGCCCTCTC
CTATCATTGAGAGTGCCAGGTCCCAGGAGGAAGTTCCCCCCAGCTCCCCTGCTCTATCACCAGGTGGAGCCCTAAGCCCT
TCAGGACACCCTTTATCATCTGCCGCAGAAGTAGTCCTCTGAACCCGCACCGCAGGTGACAAATCTGAACAATCAAAGAA
GAGAGCCTCTATCCAGAGGACCTCAGCACCCCCTAGTAGGCCTCCTCCACCCAGAGCCACCGCAAGCCCCAGGCCCTCCT
CAGGGAACATACCCTCCAGCCCTCCAGCCTCTGGAGGGGGTTCACCCACCAGCCCTAGGGCCTCCTTGGGGACTGGGACT
CCAAGTCCTAGGACCTCCCTAGAGGTCTCTCCTAATCCAGAACCACCAGAGAAGCCAGTAAGAACTCCTGAGGCCAAAGA
AAATGAAAACATCCACAATCAGAACCTCGAAGAACTTTGTACTTCCCCCACCTTAATGACATCTCAGATTGCTTCAGAGC
CTGGAGAGGCAAAGAAGATGGAAGACAAGGAAAATGATAATAAGCTTGTCTCAGCTGACTCCTCGGAGGGCCAAGACCAG
CTTAAAGTCTCCACAGTACCAGACAAGAGCAACCTCACAGCATCTGAACCTCAAGAAGAGGTATCTACAAGTGAAAAT

Alignment

ORF - retro_ptro_2049 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.5 %
• Parental protein coverage: 69.98 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ELLEELPILYNSRIGCY-VTIFQNISNLRDVFYREMSKLNHNLYEVMSKLEKQHSNKVFVVKGLSSSSRR
          .LLEELPILYNS..G...VTIFQNISNLRDVFYREMSKLNHNL.EVMSKLEKQHS.KVFVVK.LSSSSRR
Retrocopy KLLEELPILYNSHTGSM<VTIFQNISNLRDVFYREMSKLNHNLSEVMSKLEKQHSSKVFVVKRLSSSSRR

Parental  SLVISPPVQTATVSSPLTSPTSPSTLSLKSESESVSATEDLAPDAAQGEDNSEIKELLEEEEIEKEGSEA
          SLVISPPV.T.TVSSPLTSPTSPSTLS.KS.SESVSATEDLAPDAAQGEDNS.IKELLE.EEI.KEGSEA
Retrocopy SLVISPPVRTSTVSSPLTSPTSPSTLSSKSKSESVSATEDLAPDAAQGEDNS*IKELLEDEEIGKEGSEA

Parental  SSSEEDEPLPACNGPAQAQPSPTTESAKSQEEVLPSSPAPSPGGALSPSGQPSSSAAEVVLRTRTASEGS
          SSSEE.EPL..CNGP.QAQPSP..ESA.SQEEV.PSSPA.SPGGALSPSG.P.SSAAEVVL.TRTA...S
Retrocopy SSSEEEEPLLTCNGPSQAQPSPIIESARSQEEVPPSSPALSPGGALSPSGHPLSSAAEVVL*TRTAGDKS

Parental  EQPKKRASIQRTSAPPSRPPPPRATASPRPSSGNIPSSPTASGGGSPTSPRASLGTGTPSPRTSLEVSPN
          EQ.KKRASIQRTSAPPSRPPPPRATASPRPSSGNIPSSP.ASGGGSPTSPRASLGTGTPSPRTSLEVSPN
Retrocopy EQSKKRASIQRTSAPPSRPPPPRATASPRPSSGNIPSSPPASGGGSPTSPRASLGTGTPSPRTSLEVSPN

Parental  PEPPEKPVRTPEAKENENIHNQNPEELCTSPTLMTSQVASEPGEAKKMEDKEEDNKLISADSSEGQDQLQ
          PEPPEKPVRTPEAKENENIHNQN.EELCTSPTLMTSQ.ASEPGEAKKMEDKE.DNKL.SADSSEGQDQL.
Retrocopy PEPPEKPVRTPEAKENENIHNQNLEELCTSPTLMTSQIASEPGEAKKMEDKENDNKLVSADSSEGQDQLK

Parental  VFTVPENNNLTAPEPQEEVSTSEN
          V.TVP...NLTA.EPQEEVSTSEN
Retrocopy VSTVPDKSNLTASEPQEEVSTSEN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	4.52 RPM
SRP007412_cerebellum	0.00 RPM	4.30 RPM
SRP007412_heart	0.00 RPM	2.71 RPM
SRP007412_kidney	0.00 RPM	9.07 RPM
SRP007412_liver	0.03 RPM	7.89 RPM
SRP007412_testis	0.00 RPM	61.65 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2049 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2049 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2049 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2952
Pongo abelii	retro_pabe_2448

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000110934	2 retrocopies	retro_hsap_2952, retro_hsap_3192,
Gorilla gorilla	ENSGGOG00000009423	1 retrocopy	retro_ggor_1336,
Loxodonta africana	ENSLAFG00000002387	1 retrocopy	retro_lafr_1163,
Nomascus leucogenys	ENSNLEG00000017774	1 retrocopy	retro_nleu_1636,
Pongo abelii	ENSPPYG00000004526	2 retrocopies	retro_pabe_2448, retro_pabe_2648,
Pan troglodytes	ENSPTRG00000004954	2 retrocopies	retro_ptro_2049 , retro_ptro_2251,